


While I Was Away

by memoryrebel



Category: The Avengers (Marvel Movies)
Genre: Clintasha - Freeform, Emotional Hurt/Comfort, Emotional Manipulation, Hurt/Comfort, I'm Bad At Tagging, Implied/Referenced Rape/Non-con, Minor Character Death, Mistaken Identity, Non-Graphic Rape/Non-Con, Physical Abuse, Sexual Abuse, Sexual Content, Skrull(s), Stony - Freeform
Language: English
Status: In-Progress
Published: 2016-10-25
Updated: 2017-02-08
Packaged: 2018-08-27 00:42:08
Rating: Mature
Warnings: Rape/Non-Con
Chapters: 5
Words: 3,357
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/8381062
Author URL: https://archiveofourown.org/users/memoryrebel/pseuds/memoryrebel
Summary: Tony had no idea what was wrong with Steve. No clue why Steve all of a sudden felt the need to hurt him. He didn't know that Steve had been replaced by a Skrull. How could he? All he knew was that Steve was hurting him, and he couldn't stand it anymore.





	1. Hide Away

**Author's Note:**

  * Inspired by [Incursion](https://archiveofourown.org/works/2656397) by [Seaneta](https://archiveofourown.org/users/Seaneta/pseuds/Seaneta). 

**Notes for the Chapter:**

> This work was inspired by an amazing work that I read awhile ago by Seaneta. I was in love with the story, it was so well written and thought out. I thought I would like to see a different approach to the way the Skrull was handled, though, so I decided to write my own version that took a different path.  
> If you like this and want something else to read, I highly recommend reading Seaneta's version. 
> 
> Side Note: Sorry about my other fics being seemingly abandoned. I am trying to work up the motivation to go back.

     It was dark in the bathroom. But Tony didn't dare turn on the light. It might wake him.

     Tony sat quietly on the toilet lid, legs drawn up to his chest, clutching a screwdriver for dear life. He knew he was trembling but somehow couldn't stop himself. He ached all over and he just wanted it to end. He loved his boyfriend with all his heart. And while that thing out there was his boyfriend, he knew he couldn't let this go on any longer. They very fact that he was cowering in a dark bathroom and felt the need to carry the screwdriver with him at all times could attest to this having gone too far. Last night... the unthinkable. 

     Today, he would tell someone. Today, he would gather his courage and let somebody know that something was wrong. That he was being hurt and didn't know what to do. How could he? This had never happened to him before. Especially not from the man he loved. He still couldn't believe it. But the discomfort he felt that wouldn't let him so much as sit without sending tendrils of pain up his spine told him that it didn't matter whether or not he loved Steve. He had to make this stop.

     He was torn from his thoughts when he heard a soft moan coming from the bedroom.  _He's waking up,_ Tony thought wildly, rising gingerly and silently to peek through the crack in the door. In the dim light that filtered through the bedroom windows, he saw Steve stretch and reach to pat the bed beside him. The man stopped when he realized he was alone on the mattress. Steve looked up toward the door and the two locked eyes for a moment before Tony quickly stepped back, naively hoping and praying he hadn't been spotted. 

     The creaking of the bed could be heard as Steve got up, followed by the sound of feet moving over expensive, forest green carpet. As the steps grew nearer, Tony kept moving backward. He gasped when he was halted in his movement as back hit the tile wall behind him. Tony's heart was pounding in his chest as clutched the screwdriver against his chest. He didn't want to use it, but he would if he had to. 

     Suddenly light entered the bathroom through the crack in the door, leaving a little orange triangle on the wall and floor. Then the bathroom lights were turned on too, causing Tony to have to shut his eyes as they adjusted to the sudden brightness. The door creaked as Steve's hand came into view, slowly pushing the door open. 

    Once Steve's face became visible, Tony lifted his weapon away from his chest, leveling it at the man he had never thought he'd have to fear. But he was afraid of him now. He could feel the terror pumping through his entire body.

     A wicked smile appeared on Steve's face. One that didn't fit there, that possessed something Tony never thought the man capable of feeling, let alone showing. 

    "Sweetheart," came the smooth voice, "What's the matter?"

     Tony didn't answer. Steve knew what was wrong. How dare he ask that as though nothing had happened. The soldier took a step closer.

     "No!" Tony shouted as he lifted the screwdriver in Steve's direction, causing the other man to halt in his steps, "Don't come any closer."

     "Tony?" he frowned, but there was an evil glimmer in his eyes, as though he were enjoying this.

     "No! Move! Get out of my way!"

     Tony cursed himself as he heard his voice waver. Steve leaned his head forward slightly, grin growing.

     "Is that any way to speak to your boyfriend?"

     "My  _boyfriend_ ," Tony spat the word, "would never hurt me."

     "Even if you deserve it? You were being very naughty," Steve said pensively, stepping closer.

     Tony all but shouted as he stepped forward himself, brandishing his weapon. Steve stopped, looking him straight in the eye. The playful glint left and he lunged forward, grabbing Tony's wrist that held the screwdriver and twisted. Tony couldn't hold in his scream as pain shot up his arm and the screwdriver fell. Steve pushed him back against the wall and a loud crack sounded as Tony's head slammed into it. He could feel blood running down his neck. A large hand reached up, grabbing Tony's throat to keep his head back. Gasping, he looked up at his attacker. 

     Steve didn't look like Steve then. Not really. He looked like he had the past couple of weeks. No love in those eyes, only malfeasance, and wickedness. Those lifeless eyes looked right into Tony's as the soldier leaned his head forward, only breaking contact to whisper in Tony's ear.

     "Did you enjoy last night? Because I sure did. I think I was some more."

     Adrenaline coursed through Tony as he brought his knee up and hit the captain right in the groin. The main shouted as his grip loosened. Tony dove to grab the screwdriver and hit the ground hard as his leg was pulled out from under him. But he had grabbed it. 

     "Enough!" Steve shouted, dragging Tony by the ankle back toward him. The man was still on the floor as he flipped Tony onto his back and then climbed on top of him, "I said I want more. And you will give me what I want!"

     Steve noticed the screwdriver clutched in Tony's trembling hands and smiled.

     "You won't use that," he said smugly. 

     He reached his hand forward. Tony screamed. The white tile floor turned red.

**Notes for the Chapter:**

> Did you guys like it? I hope you liked it.  
> *hides*


	2. Long Ago

**Notes for the Chapter:**

> Hi everybody! Thank you for the lovely comments and kudos. They mean the world to me! I got so excited, I decided to update again today. I cannot promise that every update will come this quickly, because they most likely won't. But, enjoy it while you can. Here we go.

_He reached his hand forward. Tony screamed. The white tile floor turned red._

**-One Month Earlier-**

"I can't believe this."

     "Come on Tony, you're being dramatic."

     "Me? Dramatic? When am I ever dramatic?"

     Steve didn't answer that question with words, but sent a pointed look in his boyfriend's direction. Tony seemed to think for a moment, realizing what he had said.

     "Nevermind," he conceded, causing Steve to laugh.

     "I'll be back in three days. I promsie," Steve said, stepping forward and resting his hand on Tony's shoulder.

     Tony sighed, "You said you wouldn't go on any more missions without me. I worry about you."

     "You're worried about me?" Steve smile, quirking an eyebrow, "I'm not the one that manages to get hurt after every single mission. Despite the fact that I wear a suit of iron armor."

     Tony laughed, "Okay, mister. First of all, it's gold titatnium alloy. And second, you can drop the snarky attitude."

     "Now I'm the snarky one?" Steve gasped. Tony shut him up by pressing a quick kiss to his lips. 

     "Just promise you'll be careful."

     "I promise," Steve said, dropping the joking attitude.

     "Thank you," Tony answered, "And bring me a souvenir."

     Steve chuckled, "That I can't promise."

     "Why not?" 

     "Becasue Fury may not let me take anything, it could be classified. Or evidence. Or a myriad of other things."

    "Steve, I love it when you use words like 'myriad' on me."

     Steve laughed heartily, "Shut up."

     "Alright, go on. You're gonna be late."

     Steve stepped pulled Tony closer, moving his hands from the man's shoulder to the back of his head. He looked him straight in the eye.

     "I love you."

     Tony smiled, "I love you too. Now go, before I decide not to let you leave."

     "I'd like to see you try," Steve challenged playfully.

     He pressed a quick kiss to his boyfriend's lips before heading to the door, "I'll see you in three days."

     Tony waved as Steve disappeared out the door, then sat down on the foot of his bed.  _Three days,_ he thought,  _Everything will be fine._

**-Now-**

    "Oh my God," Tony whispered in horror, standing up quickly and backing away until he was through the doorway into his bedroom, his eyes fixed on the scene, "What have I done?"

     Steve's body was lying on the cold, porcelin tiles. The very tiles that used to be a glistening white but were now stained crimson. The soldier was lying on his back, head tilted in Tony's direction. The screwdriver was stuck in the center of his throat, blood pumping out of the open wound. Tony could feel his entire body trembling as he looked down at his hands, both of them stained with his boyfriend's blood. Movement out of the corner of his eye caused Tony to look up only to see the corpse on the floor waver slightly. Tony gasped and took quick steps backwards, only to hit the bed and fall onto his ass. It looked almost as though it was melting, before it started to change. The skin turned an icky green color, the face changed from Steve's angular face to a small, rounder one. It's hair sunk back into the head, the nose grew pointier, and the body got shorter and lost all the muscle mass. The eyes remained the same though, nothing changed about the eyes.

     "What the fuck?!" he screamed, feeling like his world was coming apart. 

     Tony could feel himself hyperventilating. He felt like he couldn't breath as his lungs struggled to pull in air. Shaking, his hands reached into his pocket and struggled to pull out his StarkPhone. He could barely hold onto to it and it fell to the floor twice before he managed to get a firm grip. 

     "J-Jarvis?" he stuttered, still gasping for air. He reached one bloody hand up to his chest.

    "Sir? Are you quite alright?"

     Tony didn't anwer at first, noticing the blood that now coated his phone, his clothes, his hands, the floor. It was everything.

     "Oh my God," he whispered again, tears falling down his face. 

     "Sir, I am going to call for assistance. Please, do not move."

     Not knowing what else to do, he dropped his phone to the floor again. He couldn't hold it in anymore, and he let great sobs escape from his body. He put his head in his hands, forgetting all the blood for a moment and just cried. His body was still trembling as he just let himself cry. There was nothing else to do. 

 

**Notes for the Chapter:**

> Ahaha! You guys thought it was Tony that got hurt, didn't you? Lol nope.   
> Anyway, hope you are enjoying my sadistic writing. More to come soon.


	3. Come Running

**Notes for the Chapter:**

> I am back! Hope y'all enjoyed your Halloween. Free candy, creepy costumes, and all that. Anyway, new chapter. Yay! Thank you guys for the great feedback, I love it. So, here ya go.

     Tony didn't hear the approaching footsteps. They were hurried and fast-paced and eventually his team came bursting through his bedroom door. 

     Despite the sudden commotion, Tony didn't look up from where he was staring down at his feet. Harsh sobs were still escaping his chest, but he was all out of tears. His eyes all dried up.

     "What the hell?" 

      That was Clint. 

     They all had stopped just inside the room. Natasha, Clint, and Bruce. Eventually, they got over the shock and went into action. Bruce saw that Tony was covered in blood and immediately came over to kneel beside his friend. Clint and Natasha saw the pool of blood in the bathroom and walked a little further into the room. Upon seeing the alien corpse on the floor, Clint repeated his explicative from before and Natasha went to investigate. 

     "Tony?" Bruce said quietly, resting a hand on the man's knee, "Tony, it's ok. You're alright."

     "This is  _not_ human, but it is definitely dead," Natasha called from beside the corpse. 

     "Thank you, Natasha, that wasn't obvious," Clint retorted.

     "Better safe than sorry," she answered, rising and exiting the bathroom, careful to avoid stepping in the pools of blood, "What happened in here, Tony?"

     Tony had managed to stop himself from crying anymore, but he hadn't yet looked up. 

     "Is he ok?" Clint asked.

     "I don't know," Bruce answered, turning his attention back to his patient, "Tony?"

     He finally looked up, his eyes red from all the tears and his face covered in bruises, "I... it was S-steve," he whispered.

     Everybody looked at the body lying on the floor, all in a myriad of confused and horrified looks. 

     "I'm sorry... what?!" Clint exclaimed.

     "H-he was Steve. But, I g-guess he wasn't Steve. And he-" Tony gulped, sniffling before looking back down.

     "He what?" Bruce asked softly.

     "What do you mean he was Steve?" Clint said at the same time. 

      Tony grabbed his head, pulling his hair, "He  _was_ Steve! Now he's not!"

     "Are you hurt, Tony?" Bruce asked, "Is that your blood?"

     "Most of it's not mine," Tony whispered, staring at the body, "He, uh... he attacked me and I..."

     "So... where's Steve?" Clint spoke up, looking to Natasha. She returned his stare for a moment, before taking her phone from her pocket and dialing quickly. Tony let out another sob.  _Steve,_ he thought,  _he must've never come back from that mission. What if he..._ He couldn't bring himself to even finish that thought.

     

**Notes for the Chapter:**

> Huh. This is shorter than expected... but my battery is dying faster than expected. Next will be longer, promise.


	4. Don't You

**Notes for the Chapter:**

> Don't you... dare judge my chapter titles. Ha!

     Not knowing what to do with the corpse, Natasha just shut the door until they could figure it all out. That way nobody would have to look at the thing. They managed to coax Tony out the room, which wasn't particularly hard since he wasn't very keen on staying there much longer. The entire room held horrible, painful memories now. The entire bed had to go, and Tony was fairly certain the clothes in the walk-in closet had to be burned now. He had always been a bit of a pyromaniac. 

     The couch in the living room was a much better location. Neutral. No evil ties to it. Good. 

     Well, since Tony now considered himself evil, that was about to change... but nobody needed to know that. Yet. Even though he hadn't actually killed Steve, he hadn't known that at the time. He was a monster. But, he couldn't dwell on that now. The real Steve was out there. He had to find him. He owed the man that much. 

     The others were being suspiciously silent. Clint was sitting beside Tony, doing his best not to comment. Bruce wasn't in the room and Tony didn't have the energy to ask where he went. Natasha was the only one making noise, but that was a hushed whisper across the room. She was on the phone, most likely with Fury. Great, now he knew too. 

     Bruce entered the room after a few minutes with a bowl of water and a washcloth. He asked Tony if he could wash the blood off Tony, and all he got was a nod. Tony didn't really understand what Bruce was asking him but had the presence of mind enough to respond at least. He didn't notice when Bruce began to gently clean Tony's face and arms and before he knew it, Bruce had finished and the bowl of water was stained red. Even though the blood was off his skin, his clothes were still drenched. These would have to go too.

     Eventually, Natasha hung up and came back to join the group.

     "Fury's gonna send some agents over here to search the tower and take the body. They're gonna look for anything suspicious then do an autopsy. Hopefully something will turn up."

     She sat down on Tony's other side, glancing sideways at him. He hadn't moved since they had sat him here.

    "Tony?"

     No response.

     They sat in silence.

**Notes for the Chapter:**

> So... this is short cause I'm running on 12% battery and out of coffee. Blegh.


	5. Nightmares

**Notes for the Chapter:**

> I am back!! I know, you either want to kill me or cry and hug me. Pick one. Both would be too much. Sorry about the hiatus. A commenter earlier pointed out that I was actually on hiatus. I will hopefully stay back. I have a computer now lol. Anyway, enjoy this extra special chapter. To make up for my absence, I wrote in some whump. Woot woot.

_Tony was working in his lab. It was peaceful or would be had his music not been blaring throughout the entire room on high volume. It was his version of peaceful. He was working on one of his cars when his music was automatically turned down, the protocol for somebody entering the lab. Pepper talked him into it when apparently everybody who came down here to talk to him later complained that it was too loud. Apparently, if somebody comes down here to talk to him, they actually want to be heard. Go figure. Tony looked up from his work to see who it was ad was dismayed to see it was Steve._

_The minute he felt it, he felt guilt as well. That was his boyfriend after all and he loved the guy. But ever since Steve had gotten back from his mission, he'd been acting strangely. Almost like he wasn't Steve anymore. Which was ridiculous. Of course, it was Steve! Maybe something happened and he was trying to rebound from that. Deal with it. Tony could understand that. And that's also partially why he felt guilty about not wanting Steve around. It wasn't Steve's fault. But, the guy was making him uncomfortable. He kept staring at him funny and wouldn't actually talk to Tony unless spoken to first. Except for today, it seemed._

_"Tony?" Steve called from just inside the doorway._

_"Yea, Cap?" Tony stood up straight, wiping his greasy hands on a rag._

_"I need to apologize."_

_Tony looked at him with a confused look on his face. Steve was just standing there staring at him, with this completely neutral look on his face._

_"For what?" Tony asked slowly, testing the waters._

_"I haven't been treating you the way a mate is supposed to treat you-"_

_"What do you mean 'mate'?"_

_"Let me finish," Steve answered, putting a hand up, "So, I am here to fix that."_

_As he spoke, Steve had moved closer to Tony, resting his hands on his shoulders and rubbing them slowly down his arms. He leaned in to kiss Tony, who returned it until Cap went to put his tongue in the inventor's mouth._

_"Hey, Cap, I appreciate the added enthusiasm but I'm trying to get some work done. Maybe later tonight?" Tony said gently, starting to back away to get back to his car._

_Steve looked at him for a moment, his grip on Tony's arms tightened. Tony looked down then back up, straight into Cap's eyes. He noticed something wrong, but couldn't quite place what. He was too focused on the pain in his arms._

_"Uh..." he laughed nervously, "Hey, Steve. You're kind of hurting me."_

_"I said I was going to do what we are supposed to do."_

_Steve pushed Tony backward quickly until he felt his lower back thump into the table. Tony acted on instinct and tried to push Steve away, lifting his arms as far as he could with his boyfriend's grip and slamming his hands on Steve's chest. His effort managed to redirect the fall, landing him and the Captain on the ground. It was a harder hit and ultimately to his disadvantage because now his boyfriend was on top of him completely, the entire weight resting on him. He tried to shove Steve off, but the man was too heavy. Steve reached further down to grip his wrists._

_"Steve! What are you doing?! Get off me!" Tony shouted, "JARVIS! Call for help!"_

_"JARVIS guessed that I came down here for mating. He said that you usually ask for cameras off when we do that, so I told him sure. I don't think he's going to be answering," Steve said as he leaned down, silencing Tony's shouts for help with a kiss. Tony tried to pull away but was unable to stop Steve from reaching down to unbuckle his jeans. Soon, they were both completely naked and Tony was shivering from fear. Steve wasn't gentle like he usually was. He entered Tony roughly and set about a brutal pace. Tony screamed._

* * *

  Tony jolted upright when he felt a hand on his shoulder. He quickly stood up, regretting it when pain shot up his back, but he had to get away. He heard voices and it took him a minute to realize they were soothing and not malicious. He looked up and realized it was Natasha and Bruce.

   "Sorry, buddy," Bruce said almost quietly, slowly coming toward Tony.

   "You were having a nightmare, Tony. We were just trying to help," Natasha added.

   It was then that Tony realized he must've fallen asleep. How could he have done that after he had just killed Captain America?  _It wasn't Steve,_ Tony tried to remind himself. He shook his head, rubbing his eyes.

   "Sorry," he muttered.

   "You have absolutely nothing to be sorry for. Come on, why not sit down? Let's all just calm down, yeah?" Bruce said, gesturing back to the couch. Tony obliged, sitting down and taking a deep breath. 

   "We need to find Steve. The real Steve."

   "We know, Tony. We're working on it," Natasha said, sounding sad. 

**Notes for the Chapter:**

> hEY all. I'll try and be back real soon. If all goes to plan, I'll update in a week at the latest. Hope y'all liked it.


End file.
